We have taken the intercoastal waterway from Barnegat Bay to Atlantic City, it is a nice ride if your not in a big hurry (or draw more then three or four feet of water). I belive there is one or two no wake zones, but there are some nice waterfront homes and boats along the way to break up the monotony. Once you get to the middle of Barnegat Bay you could overnight at Clearwater (west side of Island Beach State Park).
I have visited Clearwater many times, just never overnigted there. Anchoring is not a problem, water is pretty deep for the bay (about six to nine feet I guess). Green flies can be a problem with a light west wind (this is true almost anywhere on the bay). It does get crowded during the day on weekends, but the crowd typically thins out around 6pm.
If you wanted to stay in a slip overnight, I'm not sure who offers overnight slips. I have always docked on a lagoon, so I am not much help with local marinas.